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- PDB-5lmy: Solution structure of the m-pmv myristoylated matrix protein -

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Basic information

Entry
Database: PDB / ID: 5lmy
TitleSolution structure of the m-pmv myristoylated matrix protein
ComponentsMatrix protein p10
KeywordsVIRAL PROTEIN / Matrix / M-PMV / Myristoylated / Retrovirus
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / structural constituent of virion / nucleic acid binding / host cell cytoplasm / viral translational frameshifting / zinc ion binding / metal ion binding
Similarity search - Function
Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein ...Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesMason-Pfizer monkey virus
MethodSOLUTION NMR
AuthorsPrchal, J. / Hrabal, R.
Citation
Journal: J.Mol.Biol. / Year: 2016
Title: Membrane Interactions of the Mason-Pfizer Monkey Virus Matrix Protein and Its Budding Deficient Mutants.
Authors: Kroupa, T. / Langerova, H. / Dolezal, M. / Prchal, J. / Spiwok, V. / Hunter, E. / Rumlova, M. / Hrabal, R. / Ruml, T.
#1: Journal: J. Mol. Biol. / Year: 2012
Title: The structure of myristoylated Mason-Pfizer monkey virus matrix protein and the role of phosphatidylinositol-(4,5)-bisphosphate in its membrane binding.
Authors: Prchal, J. / Srb, P. / Hunter, E. / Ruml, T. / Hrabal, R.
History
DepositionAug 2, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionOct 5, 2016ID: 2LPY
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein p10


Theoretical massNumber of molelcules
Total (without water)14,9241
Polymers14,9241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area650 Å2
ΔGint5 kcal/mol
Surface area10160 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / -
Representative

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Components

#1: Protein Matrix protein p10


Mass: 14923.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Myristoylated Matrix protein of Mason-Pfizer Monkey Virus. N-terminaly myristoylated with C-terminal extension with 20 AA from phospohoprotein (pp24) and his-tag.
Source: (gene. exp.) Mason-Pfizer monkey virus / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07567
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D CBCA(CO)NH
141isotropic13D HN(CA)CB
151isotropic13D HBHA(CO)NH
161isotropic13D HNCO
171isotropic13D HN(CO)CA
181isotropic13D (H)CCH-TOCSY
191isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY
2112anisotropic12D 1H-15N HSQC IPAP

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.2 mM [U-99% 13C; U-99% 15N] Matrix protein p10, 100 mM potassium phosphate, 300 mM sodium chloride, 5 mM DTT, 95% H2O/5% D2O15N_13C sample95% H2O/5% D2O
filamentous virus20.2 mM [U-99% 15N] Matrix protein p10, 50 mM potassium phosphate, 150 mM sodium chloride, 5 mM DTT, 10 mg/mL Pf1 phage, 95% H2O/5% D2OAnizotropic95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMMatrix protein p10[U-99% 13C; U-99% 15N]1
100 mMpotassium phosphatenatural abundance1
300 mMsodium chloridenatural abundance1
5 mMDTTnatural abundance1
0.2 mMMatrix protein p10[U-99% 15N]2
50 mMpotassium phosphatenatural abundance2
150 mMsodium chloridenatural abundance2
5 mMDTTnatural abundance2
10 mg/mLPf1 phagenatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1600 mMstandard61 atm298 K
2300 mMAnizotropic61 atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

SoftwareName: X-PLOR / Version: NIH 2.24 / Classification: refinement
NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
Xplor-NIH2.24Schwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr Analysis2.1.5CCPNchemical shift assignment
TALOS+Cornilescu, Delaglio and Baxgeometry optimization
NMR ensembleConformers submitted total number: 15

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